Run Summary

Row

B3

12

10

3

2

Row

Table I: Summary statistics for non-failing samples generated by the nf-core/viralrecon pipeline.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

Failed Sample Summary

Row

B3

12

10

3

2

Row

Table II: Summary statistics for failing samples generated by the nf-core/viralrecon pipeline.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

SRR25426233

Row

Sample Name

SRR25426233

Genome Coverage

100

Sample Status

Pass

Row

Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.

Row

Table III. iVar Variants Summary

The summary table contains all of the variants called by iVar variants with a minimum alternate allele threshold of >=60% and a minimum read depth of 10.

This table may not exactly match the variants called in the final consensus sequence as there is a slight difference in how iVar variants and iVar consensus call them, mostly surrounding indels, along with the iVar consensus threshold being set at >=75%. The threshold difference between the two is there to hopefully catch most of these rare indel differences.

Row

Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.

Row

Figure 3. Average root-mean-square read base quality score per genomic position

Row

The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.

Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

SRR25426234

Row

Sample Name

SRR25426234

Genome Coverage

100

Sample Status

Warning

Row

Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.

Row

Table III. iVar Variants Summary

The summary table contains all of the variants called by iVar variants with a minimum alternate allele threshold of >=60% and a minimum read depth of 10.

This table may not exactly match the variants called in the final consensus sequence as there is a slight difference in how iVar variants and iVar consensus call them, mostly surrounding indels, along with the iVar consensus threshold being set at >=75%. The threshold difference between the two is there to hopefully catch most of these rare indel differences.

Row

Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.

Row

Figure 3. Average root-mean-square read base quality score per genomic position

Row

The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.

Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

SRR25426235

Row

Sample Name

SRR25426235

Genome Coverage

100

Sample Status

Pass

Row

Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.

Row

Table III. iVar Variants Summary

The summary table contains all of the variants called by iVar variants with a minimum alternate allele threshold of >=60% and a minimum read depth of 10.

This table may not exactly match the variants called in the final consensus sequence as there is a slight difference in how iVar variants and iVar consensus call them, mostly surrounding indels, along with the iVar consensus threshold being set at >=75%. The threshold difference between the two is there to hopefully catch most of these rare indel differences.

Row

Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.

Row

Figure 3. Average root-mean-square read base quality score per genomic position

Row

The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.

Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

SRR25426236

Row

Sample Name

SRR25426236

Genome Coverage

100

Sample Status

Pass

Row

Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.

Row

Table III. iVar Variants Summary

The summary table contains all of the variants called by iVar variants with a minimum alternate allele threshold of >=60% and a minimum read depth of 10.

This table may not exactly match the variants called in the final consensus sequence as there is a slight difference in how iVar variants and iVar consensus call them, mostly surrounding indels, along with the iVar consensus threshold being set at >=75%. The threshold difference between the two is there to hopefully catch most of these rare indel differences.

Row

Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.

Row

Figure 3. Average root-mean-square read base quality score per genomic position

Row

The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.

Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

SRR25426237

Row

Sample Name

SRR25426237

Genome Coverage

100

Sample Status

Pass

Row

Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.

Row

Table III. iVar Variants Summary

The summary table contains all of the variants called by iVar variants with a minimum alternate allele threshold of >=60% and a minimum read depth of 10.

This table may not exactly match the variants called in the final consensus sequence as there is a slight difference in how iVar variants and iVar consensus call them, mostly surrounding indels, along with the iVar consensus threshold being set at >=75%. The threshold difference between the two is there to hopefully catch most of these rare indel differences.

Row

Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.

Row

Figure 3. Average root-mean-square read base quality score per genomic position

Row

The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.

Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

SRR25426267

Row

Sample Name

SRR25426267

Genome Coverage

0

Sample Status

Failed

Row

Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.

Row

Table III. iVar Variants Summary

The summary table contains all of the variants called by iVar variants with a minimum alternate allele threshold of >=60% and a minimum read depth of 10.

This table may not exactly match the variants called in the final consensus sequence as there is a slight difference in how iVar variants and iVar consensus call them, mostly surrounding indels, along with the iVar consensus threshold being set at >=75%. The threshold difference between the two is there to hopefully catch most of these rare indel differences.

Row

Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.

Row

Figure 3. Average root-mean-square read base quality score per genomic position

Row

The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.

Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

SRR25426268

Row

Sample Name

SRR25426268

Genome Coverage

0

Sample Status

Failed

Row

Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.

Row

Table III. iVar Variants Summary

The summary table contains all of the variants called by iVar variants with a minimum alternate allele threshold of >=60% and a minimum read depth of 10.

This table may not exactly match the variants called in the final consensus sequence as there is a slight difference in how iVar variants and iVar consensus call them, mostly surrounding indels, along with the iVar consensus threshold being set at >=75%. The threshold difference between the two is there to hopefully catch most of these rare indel differences.

Row

Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.

Row

Figure 3. Average root-mean-square read base quality score per genomic position

Row

The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.

Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

SRR25426269

Row

Sample Name

SRR25426269

Genome Coverage

100

Sample Status

Warning

Row

Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.

Row

Table III. iVar Variants Summary

The summary table contains all of the variants called by iVar variants with a minimum alternate allele threshold of >=60% and a minimum read depth of 10.

This table may not exactly match the variants called in the final consensus sequence as there is a slight difference in how iVar variants and iVar consensus call them, mostly surrounding indels, along with the iVar consensus threshold being set at >=75%. The threshold difference between the two is there to hopefully catch most of these rare indel differences.

Row

Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.

Row

Figure 3. Average root-mean-square read base quality score per genomic position

Row

The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.

Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

SRR26064243

Row

Sample Name

SRR26064243

Genome Coverage

100

Sample Status

Warning

Row

Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.

Row

Table III. iVar Variants Summary

The summary table contains all of the variants called by iVar variants with a minimum alternate allele threshold of >=60% and a minimum read depth of 10.

This table may not exactly match the variants called in the final consensus sequence as there is a slight difference in how iVar variants and iVar consensus call them, mostly surrounding indels, along with the iVar consensus threshold being set at >=75%. The threshold difference between the two is there to hopefully catch most of these rare indel differences.

Row

Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.

Row

Figure 3. Average root-mean-square read base quality score per genomic position

Row

Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

SRR26544933

Row

Sample Name

SRR26544933

Genome Coverage

100

Sample Status

Pass

Row

Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.

Row

Table III. iVar Variants Summary

The summary table contains all of the variants called by iVar variants with a minimum alternate allele threshold of >=60% and a minimum read depth of 10.

This table may not exactly match the variants called in the final consensus sequence as there is a slight difference in how iVar variants and iVar consensus call them, mostly surrounding indels, along with the iVar consensus threshold being set at >=75%. The threshold difference between the two is there to hopefully catch most of these rare indel differences.

Row

Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.

Row

Figure 3. Average root-mean-square read base quality score per genomic position

Row

Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

SRR26544934

Row

Sample Name

SRR26544934

Genome Coverage

100

Sample Status

Pass

Row

Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.

Row

Table III. iVar Variants Summary

The summary table contains all of the variants called by iVar variants with a minimum alternate allele threshold of >=60% and a minimum read depth of 10.

This table may not exactly match the variants called in the final consensus sequence as there is a slight difference in how iVar variants and iVar consensus call them, mostly surrounding indels, along with the iVar consensus threshold being set at >=75%. The threshold difference between the two is there to hopefully catch most of these rare indel differences.

Row

Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.

Row

Figure 3. Average root-mean-square read base quality score per genomic position

Row

Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

SRR26544935

Row

Sample Name

SRR26544935

Genome Coverage

100

Sample Status

Pass

Row

Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.

Row

Table III. iVar Variants Summary

The summary table contains all of the variants called by iVar variants with a minimum alternate allele threshold of >=60% and a minimum read depth of 10.

This table may not exactly match the variants called in the final consensus sequence as there is a slight difference in how iVar variants and iVar consensus call them, mostly surrounding indels, along with the iVar consensus threshold being set at >=75%. The threshold difference between the two is there to hopefully catch most of these rare indel differences.

Row

Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.

Row

Figure 3. Average root-mean-square read base quality score per genomic position

Row

Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

In-Depth Results

Row

Consensus Files

MultiQC

Nextclade

Row

FastQC

VCF Files

BAM/BAI Files

Row

Depth Files

Quality Files

Variant Annotations

Row

Kraken2

Quast Report

FastP

Row

Report generated using MeaSeq on 2025-04-04 - © Government of Canada, Public Health Agency of Canada, National Microbiology Laboratory

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